Hi Thomas ! Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon values etc. values. Where to get these values
Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot <[email protected]>wrote: > Not sure about amb2gmx.pl or acpypi but you can do this by hand. Consult > the GROMACS manual (Chapter 4) for the equations to convert the parameters > into GROMACS format. > > I would also say that the easiest way would be to create a new entry in the > .rtp and then also add the appropriate bonded parameters into the bon.itp > file, making sure to include the bonded parameters for the new O3 atom type. > Do note that you need to also add this new atom type for the O3 oxygen into > the .atp file and the non-bonded parameters for the atom type into the > nb.itp file. > > You can also add entries into the .hdb to allow pdb2gmx to add the > appropriate hydrogens to your ATP if so desired. If not, your input pdb for > pdb2gmx will need to have these hydrogens already included. > > Cheers > > Tom > > Chandan Choudhury wrote: > >> Hello gmx users, >> I need to use ATP's parameter for amber port in gromacs. The atp.prep and >> frcmod.phos for ATP can be found at >> http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in >> ffamber. >> The program amb2gmx.pl <http://amb2gmx.pl> needs amber to be installed, >> which is not present. Same with ACPYPI. >> >> >> Any suggestion will be very helpful. >> >> Chandan >> >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> > -- > Thomas Piggot > University of Bristol, UK. > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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